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The Chew Bahir Drilling Project (CBDP) aims to test possible linkages between climate and evolution in Africa through the analysis of sediment cores that have recorded environmental changes in the Chew Bahir basin. In this statistical project we consider the Chew Bahir palaeolake to be a dynamical system consisting of interactions between its different components, such as the waterbody, the sediment beneath lake, and the organisms living within and around the lake. Recurrence is a common feature of such dynamical systems, with recurring patterns in the state of the system reflecting typical influences. Identifying and defining these influences contributes significantly to our understanding of the dynamics of the system. Different recurring changes in precipitation, evaporation, and wind speed in the Chew Bahir basin could result in similar (but not identical) conditions in the lake (e.g., depth and area of the lake, alkalinity and salinity of the lake water, species assemblages in the water body, and diagenesis in the sediments). Recurrence plots (RPs) are graphic displays of such recurring states within a system. Measures of complexity were subsequently introduced to complement the visual inspection of recurrence plots, and provide quantitative descriptions for use in recurrence quantification analysis (RQA). We present and discuss herein results from an RQA on the environmental record from six short (< 17 m) sediment cores collected during the CBDP, spanning the last 45 kyrs. The different types of variability and transitions in these records were classified to improve our understanding of the response of the biosphere to climate change, and especially the response of humans in the area.
Abrupt or gradual?
(2018)
We used a change point analysis on a late Pleistocene-Holocene lake-sediment record from the Chew Bahir basin in the southern Ethiopian Rift to determine the amplitude and duration of past climate transitions. The most dramatic changes occurred over 240 yr (from similar to 15,700 to 15,460 yr) during the onset of the African Humid Period (AHP), and over 990 yr (from similar to 4875 to 3885 yr) during its protracted termination. The AHP was interrupted by a distinct dry period coinciding with the high-latitude Younger Dryas stadial, which had an abrupt onset (less than similar to 100 yr) at similar to 13,260 yr and lasted until similar to 11,730 yr. Wet-dry-wet transitions prior to the AHP may reflect the high-latitude Dansgaard-Oeschger cycles, as indicated by cross-correlation of the potassium record with the NorthGRIP ice core record between similar to 45-20 ka. These findings may contribute to the debates regarding the amplitude, and duration and mechanisms of past climate transitions, and their possible influence on the development of early modern human cultures.
Modern mobile devices (i.e. smartphones and tablet computers) are widespread, everyday tools, which are equipped with a variety of sensors including three-axis magnetometers. Here, we investigate the feasibility and the potential of using such mobile devices to mimic geophysical experiments in the classroom in a table-top setup. We focus on magnetic surveying and present a basic setup of a table-top experiment for collecting three-component magnetic data across well-defined source bodies and structures. Our results demonstrate that the quality of the recorded data is sufficient to address a number of important basic concepts in the magnetic method. The shown examples cover the analysis of magnetic data recorded across different kinds of dipole sources, thus illustrating the complexity of magnetic anomalies. In addition, we analyze the horizontal resolution capabilities using a pair of dipole sources placed at different horizontal distances to each other. Furthermore, we demonstrate that magnetic data recorded with a mobile device can even be used to introduce filtering, transformation, and inversion approaches as they are typically used when processing magnetic data sets recorded for real-world field applications. Thus, we conclude that such table-top experiments represent an easy-to-implement experimental procedure (as student exercise or classroom demonstration) and can provide first hands-on experience in the basic principles of magnetic surveying including the fundamentals of data acquisition, analysis and processing, as well as data evaluation and interpretation.
The actual evapotranspiration is an important, but difficult to determine, element in the water balance of lakes and their catchment areas. Reliable data on evapotranspiration are not available for most lake basins for which paleoclimate reconstructions and modeling have been performed, particularly those in remote parts of Africa. We have used thermal infrared multispectral data for 14 ASTER scenes from the TERRA satellite to estimate the actual evapotranspiration in the 12,800 km(2) catchment of the Suguta Valley, northern Kenya Rift Evidence from sediments and paleo-shorelines indicates that, during the African Humid Period (AHP, 14.8 to 5.5 kyrs BP), this valley contained a large lake, 280 m deep and covering similar to 2200 km(2), which has now virtually disappeared. Evapotranspiration estimates for the Suguta Basin were generated using the Surface Energy Balance Algorithm for Land (SEBAL). Climate data required for the model were extracted from a high-resolution gridded dataset obtained from the Climatic Research Unit (East Anglia, UK). Results suggest significant spatial variations in evapotranspiration within the catchment area (ranging from 450 mm/yr in the basin to the north to 2000 mm/yr in more elevated areas) and precipitation that was similar to 20% higher during the AHP than in recent times. These results are in agreement with other estimates of paleo-precipitation in East Africa. The extreme response of the lake system (similar to 280 m greater water depth than today, and a lake surface area of 2200 km(2)) to only moderately higher precipitation illustrates the possible sensitivity of this area to future climate change.
Python is used in a wide range of geoscientific applications, such as in processing images for remote sensing, in generating and processing digital elevation models, and in analyzing time series. This book introduces methods of data analysis in the geosciences using Python that include basic statistics for univariate, bivariate, and multivariate data sets, time series analysis, and signal processing; the analysis of spatial and directional data; and image analysis. The text includes numerous examples that demonstrate how Python can be used on data sets from the earth sciences. The supplementary electronic material (available online through Springer Link) contains the example data as well as recipes that include all the Python commands featured in the book.
Spectral analysis is a technique of time-series analysis that decomposes signals into linear combinations of harmonic components. Rooted in the 19th century, spectral analysis gained popularity in palaeoclimatology since the early 1980s. This was partly due to the availability of long time series of past climates, but also the development of new, partly adapted methods and the increasing spread of affordable personal computers. This paper reviews the most important methods of spectral analysis for palaeoclimate time series and discusses the prerequisites for their application as well as advantages and disadvantages. The paper also offers an overview of suitable software, as well as computer code for using the methods on synthetic examples.
Using molecular genetic methods and an ancient DNA approach, we studied population and species succession of rotifers of the genus Brachionus in the Kenyan alkaline-saline crater lake Sonachi since the beginning of the 19th century as well as distribution of Brachionus haplotypes in recent and historic sediments of other lakes of the East African Rift System. The sediment core record of Lake Sonachi displays haplotypes of a distinct evolutionary lineage in all increments. Populations were dominated by a single mitochondrial haplotype for a period of 150 years, and two putatively intraspecific turnovers in dominance occurred. Both changes are concordant with major environmental perturbations documented by a profound visible change in sediment composition of the core. The first change was very abrupt and occurred after the deposition of volcanic ash at the beginning of the 19th century. The second change coincides with a major lake level lowstand during the 1940s. It was preceded by a period of successively declining lake level, in which two other haplotypes appeared in the lake. One of these putatively belongs to another species documented in historical and recent Kenyan lake sediments. The analysis of plankton population dynamics through historical time can reveal patterns of population persistence and turnover in relation to environmental changes.
Lake Naivasha, Kenya, is one of a number of freshwater lakes in the East African Rift System. Since the beginning of the twentieth century, it has experienced greater anthropogenic influence as a result of increasingly intensive farming of coffee, tea, flowers, and other horticultural crops within its catchment. The water-level history of Lake Naivasha over the past 200 years was derived from a combination of instrumental records and sediment data. In this study, we analysed diatoms in a lake sediment core to infer past lacustrine conductivity and total phosphorus concentrations. We also measured total nitrogen and carbon concentrations in the sediments. Core chronology was established by (210)Pb dating and covered a similar to 186-year history of natural (climatic) and human-induced environmental changes. Three stratigraphic zones in the core were identified using diatom assemblages. There was a change from littoral/epiphytic diatoms such as Gomphonema gracile and Cymbella muelleri, which occurred during a prolonged dry period from ca. 1820 to 1896 AD, through a transition period, to the present planktonic Aulacoseira sp. that favors nutrient-rich waters. This marked change in the diatom assemblage was caused by climate change, and later a strong anthropogenic overprint on the lake system. Increases in sediment accumulation rates since 1928, from 0.01 to 0.08 g cm(-2) year(-1) correlate with an increase in diatom-inferred total phosphorus concentrations since the beginning of the twentieth century. The increase in phosphorus accumulation suggests increasing eutrophication of freshwater Lake Naivasha. This study identified two major periods in the lake's history: (1) the period from 1820 to 1950 AD, during which the lake was affected mainly by natural climate variations, and (2) the period since 1950, during which the effects of anthropogenic activity overprinted those of natural climate variation.
Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approximately 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based denaturing high-performance liquid chromatography (DHPLC). An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length and if the amplicons differed only in a small number of nucleotides. Generally, the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.
Hidden diversity in diatoms of Kenyan Lake Naivasha a genetic approach detects temporal variation
(2012)
This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (7667 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated with environmental factors.
Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.
MATLAB is used in a wide range of applications in geosciences, such as image processing in remote sensing, generation and processing of digital elevation models and the analysis of time series. This book introduces basic methods of data analysis in geosciences using MATLAB. The text includes a brief description of each method and numerous examples demonstrating how MATLAB can be used on data sets from earth sciences. All MATLAB recipes can be easily modified in order to analyse the reader's own data sets. The book comes with a CD containing exemplary data sets and a digital version of the MATLAB recipes. (Springer)
MATLAB is used in a wide range of applications in geosciences, such as image processing in remote sensing, generation and processing of digital elevation models and the analysis of time series. This book introduces basic methods of data analysis in geosciences using MATLAB. The text includes a brief description of each method and numerous examples on how MATLAB can be used on data sets from earth sciences. All MATLAB recipes can easily be modified in order to analyse the reader's own data sets. The book comes with a CD containing example data sets and a digital version of the MATLAB recipes.
Three diatomite beds exposed in the Ol Njorowa Gorge south of Lake Naivasha, Central Kenya Rift, document three major lake-level highstands between 175 and 60 kyr BP. Diatom transfer-function estimates of hydrological and hydrochemical parameters suggest that a deep and large freshwater lake existed during the highstands at 135 and 80 kyr BP. In contrast, a shallower but more expanded freshwater lake existed at 110 kyr BP. The best analog for the most extreme highstand at 135 kyr BP is the highstand during the Early Holocene humid period from 10 to 6 kyr BP. The environmental conditions as reconstructed from diatom assemblages suggest long-lasting episodes of increased humidity during the high lake periods. This contrasts to the modern situation with a relatively shallow Lake Naivasha characterized by rapid water level fluctuations within a few decades. The most likely cause for the variable hydrological conditions since 175 kyr BP is orbitally driven insolation changes on the equator and increased lateral moisture transport from the ocean.
Higher variability in rainfall and river discharge could be of major importance in landslide generation in the north-western Argentine Andes. Annual layered (varved) deposits of a landslide dammed lake in the Santa Maria Basin (26°S, 66°W) with an age of 30,000 14C years provide an archive of precipitation variability during this time. The comparison of these data with present-day rainfall observations tests the hypothesis that increased rainfall variability played a major role in landslide generation. A potential cause of such variability is the El Niño/ Southern Oscillation (ENSO). The causal link between ENSO and local rainfall is quantified by using a new method of nonlinear data analysis, the quantitative analysis of cross recurrence plots (CRP). This method seeks similarities in the dynamics of two different processes, such as an ocean-atmosphere oscillation and local rainfall. Our analysis reveals significant similarities in the statistics of both modern and palaeo-precipitation data. The similarities in the data suggest that an ENSO-like influence on local rainfall was present at around 30,000 14C years ago. Increased rainfall, which was inferred from a lake balance modeling in a previous study, together with ENSO-like cyclicities could help to explain the clustering of landslides at around 30,000 14C years ago.
During the last 5 Ma the Earth's ocean-atmosphere system passed through several major transitions, many of which are discussed as possible triggers for human evolution. A classic in this context is the possible influence of the closure of the Panama Strait, the intensification of Northern Hemisphere Glaciation, a stepwise increase in aridity in Africa, and the first appearance of the genus Homo about 2.5 - 2.7 Ma ago. Apart from the fact that the correlation between these events does not necessarily imply causality, many attempts to establish a relationship between climate and evolution fail due to the challenge of precisely localizing an a priori unknown number of changes potentially underlying complex climate records. The kernel-based Bayesian inference approach applied here allows inferring the location, generic shape, and temporal scale of multiple transitions in established records of Plio-Pleistocene African climate. By defining a transparent probabilistic analysis strategy, we are able to identify conjoint changes occurring across the investigated terrigenous dust records from Ocean Drilling Programme (ODP) sites in the Atlantic Ocean (ODP 659), Arabian (ODP 721/722) and Mediterranean Sea (ODP 967). The study indicates a two-step transition in the African climate proxy records at (2.35-2.10) Ma and (1.70 - 1.50) Ma, that may be associated with the reorganization of the Hadley-Walker Circulation. .
The Pleistocene archeological record in East Africa has revealed unusual accumulations of Acheulean handaxes at prehistoric sites. In particular, there has been intensive debate concerning whether the artifact accumulation at the Middle Pleistocene Olorgesailie (Southern Kenya Rift) and Kariandusi (Central Kenya Rift) sites were a result of fluvial reworking or of in situ deposition by hominids. We used a two-step approach to test the hypothesis of fluvial reworking. Firstly, the behavior of handaxes in water currents was investigated in a current flume and the flow threshold required to reorientate the handaxes was determined. The results of these experiments suggested that, in relatively high energy and non-steady flow conditions, handaxes will reorientate themselves perpendicular to the current direction. Secondly, an automated image analysis routine was developed and applied to archeological plans from three Acheulean sites, two at Olorgesailie and one at Kariandusi, in order to determine the orientations of the handaxes. A Rayleigh test was then applied to the orientation data to test for a preferred orientation. The results revealed that the handaxes at the Upper Kariandusi Site and the Olorgesailie Main Site Mid Trench had a preferential orientation, suggesting reworking by a paleocurrent. The handaxes from the Olorgesailie Main Site H/6A, however, appeared to be randomly oriented and in situ deposition by the producers therefore remains a possibility.